public class CharactersDataUnalignedBlockHandler extends AbstractNexusBlockHandler implements NexusBlockHandler, ReadWriteConstants, NexusConstants
CHARACTERS, DATA or UNALIGNED
blocks.ATTRIBUTE_STRING_KEY, ATTRIBUTES_NAMESPACE_FOLDER, DATA_TYPE_NAMESPACE_FOLDER, DATA_TYPE_SIMPLE_VALUE_LIST, DEFAULT_CHAR_SET_ID_PREFIX, DEFAULT_CHARACTER_DEFINITION_ID_PREFIX, DEFAULT_EDGE_ID_PREFIX, DEFAULT_GENERAL_ID_PREFIX, DEFAULT_MATRIX_ID_PREFIX, DEFAULT_MAX_COMMENT_LENGTH, DEFAULT_MAX_TOKENS_TO_READ, DEFAULT_META_ID_PREFIX, DEFAULT_NETWORK_ID_PREFIX, DEFAULT_NODE_EDGE_SET_ID_PREFIX, DEFAULT_NODE_ID_PREFIX, DEFAULT_OTU_ID_PREFIX, DEFAULT_OTU_LIST_ID_PREFIX, DEFAULT_OTU_SET_ID_PREFIX, DEFAULT_SEQUENCE_ID_PREFIX, DEFAULT_SEQUENCE_SET_ID_PREFIX, DEFAULT_TOKEN_DEFINITION_ID_PREFIX, DEFAULT_TOKEN_SET_ID_PREFIX, DEFAULT_TREE_ID_PREFIX, DEFAULT_TREE_NETWORK_GROUP_ID_PREFIX, DEFAULT_TREE_NETWORK_SET_ID_PREFIX, JPHYLOIO_ATTRIBUTES_NAMESPACE, JPHYLOIO_ATTRIBUTES_PREFIX, JPHYLOIO_DATA_TYPE_NAMESPACE, JPHYLOIO_DATA_TYPE_PREFIX, JPHYLOIO_FORMATS_NAMESPACE_PREFIX, JPHYLOIO_GENERAL_NAMESPACE, JPHYLOIO_NAMESPACE_PREFIX, JPHYLOIO_PREDICATE_NAMESPACE, JPHYLOIO_PREDICATE_PREFIX, PREDICATE_CHARACTER_COUNT, PREDICATE_EDGE_LENGTH, PREDICATE_EDGE_SOURCE_NODE, PREDICATE_EDGE_TARGET_NODE, PREDICATE_HAS_CUSTOM_XML, PREDICATE_HAS_LITERAL_METADATA, PREDICATE_HAS_RESOURCE_METADATA, PREDICATE_IS_CROSSLINK, PREDICATE_NAMESPACE_FOLDER, PREDICATE_PART_SEPERATOR, PREDICATE_SEQUENCE_COUNT, RESERVED_ID_PREFIXALTERNATIVE_END_COMMAND, BEGIN_COMMAND, BLOCK_NAME_CHARACTERS, BLOCK_NAME_DATA, BLOCK_NAME_NETWORKS, BLOCK_NAME_SETS, BLOCK_NAME_TAXA, BLOCK_NAME_TREES, BLOCK_NAME_UNALIGNED, CHARACTER_NAME_STATES_SEPARATOR, COMMAND_END, COMMAND_NAME_CHAR_LABELS, COMMAND_NAME_CHAR_SET, COMMAND_NAME_CHAR_STATE_LABELS, COMMAND_NAME_DIMENSIONS, COMMAND_NAME_FORMAT, COMMAND_NAME_LINK, COMMAND_NAME_MATRIX, COMMAND_NAME_NETWORK, COMMAND_NAME_TAX_LABELS, COMMAND_NAME_TAXON_SET, COMMAND_NAME_TITLE, COMMAND_NAME_TRANSLATE, COMMAND_NAME_TREE, COMMAND_NAME_TREE_SET, COMMENT_END, COMMENT_START, DIMENSIONS_SUBCOMMAND_NCHAR, DIMENSIONS_SUBCOMMAND_NEW_TAXA, DIMENSIONS_SUBCOMMAND_NTAX, ELEMENT_SEPARATOR, END_COMMAND, FIRST_LINE, FORMAT_NAME_STANDARD, FORMAT_NAME_VECTOR, FORMAT_SUBCOMMAND_DATA_TYPE, FORMAT_SUBCOMMAND_GAP_CHAR, FORMAT_SUBCOMMAND_INTERLEAVE, FORMAT_SUBCOMMAND_MATCH_CHAR, FORMAT_SUBCOMMAND_MISSING_CHAR, FORMAT_SUBCOMMAND_NO_LABELS, FORMAT_SUBCOMMAND_NO_TOKENS, FORMAT_SUBCOMMAND_SYMBOLS, FORMAT_SUBCOMMAND_TOKENS, FORMAT_SUBCOMMAND_TRANSPOSE, FORMAT_VALUE_CONTINUOUS_DATA_TYPE, FORMAT_VALUE_DNA_DATA_TYPE, FORMAT_VALUE_MIXED_DATA_TYPE, FORMAT_VALUE_NUCLEOTIDE_DATA_TYPE, FORMAT_VALUE_PROTEIN_DATA_TYPE, FORMAT_VALUE_RNA_DATA_TYPE, FORMAT_VALUE_STANDARD_DATA_TYPE, KEY_VALUE_SEPARATOR, MATRIX_POLYMORPHIC_TOKEN_END, MATRIX_POLYMORPHIC_TOKEN_START, MATRIX_UNCERTAINS_TOKEN_END, MATRIX_UNCERTAINS_TOKEN_START, NEXUS_FORMAT_NAME, NEXUS_NAMESPACE_PREFIX, NEXUS_PREDICATE_NAMESPACE, SET_END_INDEX_SYMBOL, SET_KEY_WORD_ALL, SET_KEY_WORD_REMAINING, SET_REGULAR_INTERVAL_SYMBOL, SET_TO_SYMBOL, SET_VECTOR_CONTAINED, SET_VECTOR_NOT_CONTAINED, UNTIL_WHITESPACE_COMMENT_COMMAND_EQUAL_PATTERN, UNTIL_WHITESPACE_COMMENT_COMMAND_PATTERN, VALUE_DELIMITER, WORD_DELIMITER| Constructor and Description |
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CharactersDataUnalignedBlockHandler() |
| Modifier and Type | Method and Description |
|---|---|
void |
beforeCommand(NexusReaderStreamDataProvider streamDataProvider,
java.lang.String commandName,
NexusCommandEventReader commandReader)
This method is called before a command found in a block handled by this handler is processed,
by calling the according command reader.
|
void |
handleBegin(NexusReaderStreamDataProvider streamDataProvider)
This method will be called by
NexusEventReader each time a BEGIN command for
a block listed in NexusBlockHandler.getBlockNames() is read. |
void |
handleEnd(NexusReaderStreamDataProvider streamDataProvider)
This method will be called by
NexusEventReader each time an END command for
a block listed in NexusBlockHandler.getBlockNames() is read. |
getBlockNamesclone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitgetBlockNamespublic CharactersDataUnalignedBlockHandler()
public void handleBegin(NexusReaderStreamDataProvider streamDataProvider)
NexusBlockHandlerNexusEventReader each time a BEGIN command for
a block listed in NexusBlockHandler.getBlockNames() is read.handleBegin in interface NexusBlockHandlerstreamDataProvider - the stream data provider of the calling NexusEventReaderAbstractEventReader.getStreamDataProvider()public void handleEnd(NexusReaderStreamDataProvider streamDataProvider)
NexusBlockHandlerNexusEventReader each time an END command for
a block listed in NexusBlockHandler.getBlockNames() is read.handleEnd in interface NexusBlockHandlerstreamDataProvider - the stream data provider of the calling NexusEventReaderAbstractEventReader.getStreamDataProvider()public void beforeCommand(NexusReaderStreamDataProvider streamDataProvider, java.lang.String commandName, NexusCommandEventReader commandReader)
NexusBlockHandlerbeforeCommand in interface NexusBlockHandlerstreamDataProvider - the stream data provider of the calling NexusEventReadercommandName - the name of the Nexus command, that will be processed nextcommandReader - the reader that will be used to process this command or null if
no according reader was foundAbstractEventReader.getStreamDataProvider()